Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Kiyoshi Oguri

Research output: Contribution to journalConference articlepeer-review

3 Citations (Scopus)


This paper discusses design methodology of high-throughput arithmetic pipeline modules for an FPGA-based biochemical simulator. Since limitation of data-input bandwidth caused by port constraints often has a negative impact on pipeline scheduling results, we propose a priority assignment method of input data which enables efficient arithmetic pipeline scheduling under given input port constraints. Evaluation results with frequently used rate-law functions in biochemical models revealed that the proposed method achieved shorter latency compared to ASAP and ALAP scheduling with random input orders, reducing hardware costs by 17.57 % and by 27.43 % on average, respectively.

Original languageEnglish
Pages (from-to)368-373
Number of pages6
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Publication statusPublished - 2009
Event5th International Workshop of Applied Reconfigurable Computing, ARC 2009 - Karlsruhe, United States
Duration: 2009 Mar 162009 Mar 18

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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